Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti

A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways inSinorhizobium meliloti

(2017) George C. diCenzo et al.   GENETICS

The Divided Bacterial Genome: Structure, Function, and Evolution

(2017) George C. diCenzo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago–Sinorhizobium meliloti Symbiosis

(2017) George C. diCenzo et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

(2017) Jennifer A. Bartell et al.   Nature Communications

Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements

(2017) Chelsie E. Armbruster et al.   PLoS Pathogens

A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways inSinorhizobium meliloti

(2017) George C. diCenzo et al.   GENETICS

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

(2017) Byoung-Mo Koo et al.   Cell Systems

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

(2017) Brian T. Burger et al.   mSystems

Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

(2016) Nikki E. Freed et al.   BMC MICROBIOLOGY

Genomic resources for identification of the minimal N2 -fixing symbiotic genome

(2016) George C. diCenzo et al.   ENVIRONMENTAL MICROBIOLOGY

Role of O 2 in the Growth of Rhizobium leguminosarum bv. viciae 3841 on Glucose and Succinate

(2016) Rachel M. Wheatley et al.   JOURNAL OF BACTERIOLOGY

The design and analysis of transposon insertion sequencing experiments

(2016) Michael C. Chao et al.   NATURE REVIEWS MICROBIOLOGY

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

(2016) Jared T. Broddrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti

(2016) George C. diCenzo et al.   Nature Communications

The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum

(2016) Benjamin J. Perry et al.   Frontiers in Microbiology

Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks

(2015) Aditya Pratapa et al.   BIOINFORMATICS

Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability

(2015) Gaowen Liu et al.   CELL

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris

(2015) Kieran B. Pechter et al.   JOURNAL OF BACTERIOLOGY

Effects of synthetic large-scale genome reduction on metabolism and metabolic preferences in a nutritionally complex environment

(2015) Fan Fei et al.   Metabolomics

Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome

(2015) George C. diCenzo et al.   MOLECULAR GENETICS AND GENOMICS

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

General and condition-specific essential functions ofPseudomonas aeruginosa

(2015) Samuel A. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

(2015) Marco Galardini et al.   PLoS Computational Biology

The differential view of genotype–phenotype relationships

(2015) Virginie Orgogozo et al.   Frontiers in Genetics

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

(2014) Travis J Wheeler et al.   BMC BIOINFORMATICS

Construction of a mariner-based transposon vector for use in insertion sequence mutagenesis in selected members of the Rhizobiaceae

(2014) Benjamin J Perry et al.   BMC MICROBIOLOGY

Key roles of microsymbiont amino acid metabolism in rhizobia-legume interactions

(2014) Michael Frederick Dunn   CRITICAL REVIEWS IN MICROBIOLOGY

Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering

(2014) M. Juhas et al.   MICROBIOLOGY-SGM

Identification of essential alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems

(2014) Patrick D. Curtis et al.   MOLECULAR MICROBIOLOGY

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

(2014) Hong Yang et al.   PLoS Computational Biology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

(2014) George C. diCenzo et al.   PLoS Genetics

Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

(2013) Marco Galardini et al.   Genome Biology and Evolution

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries

(2013) David Skurnik et al.   PLoS Pathogens

High-throughput comparison of gene fitness among related bacteria

(2012) Rocio Canals et al.   BMC GENOMICS

The tRNAargGene andengAAre Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

(2012) George diCenzo et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability

(2012) Tobias Bergmiller et al.   PLoS Genetics

Insertion site preference of Mu, Tn5, and Tn7 transposons

(2012) Brian Green et al.   Mobile DNA

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

(2011) L. A. Gallagher et al.   mBio

Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of Escherichia coli Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery

(2010) L. Ferrieres et al.   JOURNAL OF BACTERIOLOGY

FeuN, a novel modulator of two-component signalling identified in Sinorhizobium meliloti

(2010) Rebecca E. Carlyon et al.   MOLECULAR MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

Increased Malonyl Coenzyme A Biosynthesis by Tuning the Escherichia coli Metabolic Network and Its Application to Flavanone Production

(2009) Z. L. Fowler et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic systems biology

(2009) Bernhard Palsson   FEBS LETTERS

Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

(2009) Hong Guo et al.   GENOME

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

(2009) S. C. Slater et al.   JOURNAL OF BACTERIOLOGY

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms

(2009) Tim van Opijnen et al.   NATURE METHODS

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

ASinorhizobium melilotiosmosensory two-component system required for cyclic glucan export and symbiosis

(2008) Joel S. Griffitts et al.   MOLECULAR MICROBIOLOGY

A symbiotic mutant of Sinorhizobium meliloti reveals a novel genetic pathway involving succinoglycan biosynthetic functions

(2008) Joel S. Griffitts et al.   MOLECULAR MICROBIOLOGY

eSGA: E. coli synthetic genetic array analysis

(2008) Gareth Butland et al.   NATURE METHODS

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

The repABC plasmid family

(2008) Miguel A. Cevallos et al.   PLASMID